The present invention is in the field of virology. The invention relates to the nucleic acid sequence of the complete genome of the new simian immunodeficiency virus isolate from a red-capped mangabey, SIVrcm, and nucleic acids derived therefrom. The invention also relates to peptides encoded by and/or derived from SIVrcm nucleic acid sequences, and host cells containing these nucleic acid sequences and peptides. The invention also relates to diagnostic methods, kits and immunogens which employ the nucleic acids, peptides and/or host cells of the invention.
Phylogenetic analyses of simian immunodeficiency virus (SIV) isolates reveal that they belong to five distinct lineages of the lentivirus family of retroviruses (47). These five SIV lentiviral lineages form a distinct sub-group because primate viruses are more closely related to each other than to lentiviruses from non-primate hosts (47). Importantly, only simian species indigenous to the African continent are naturally infected (4, 13, 28, 35). Thus far, natural SIV infections in Africa have been documented in the sooty mangabey (SM) (Cercocebus torquatus atys) (SIVsm strains), in Liberia (30), in Sierra Leone (4, 5), and the Ivory Coast (43); in all four sub-species of African green monkeys (agm) (Cercopithecus aethiops) (1, 21, 22, 25, 33, 34, 39) (SIVagm strains), in eastern, central and western Africa; in the Sykes monkey (syk) (Cercopithecus mitis) (SIVsyk strains) in Kenya (9); in the mandrill (mnd) (Mandrillus sphinx) (SIVmmd strains) (38, 50) in Gabon; and in chimpanzees (cpz) (Pan troglodytes) (SIVcpz strains) (19, 20, 41, 42) also from Gabon. Because these SIVs and their simian hosts are highly divergent from each other and widely distributed across Africa, it is believed that the SIV family evolved and established itself in African simians long before acquired immunodeficiency syndrome (AIDS) appeared in humans (4, 15, 18, 19, 21, 30, 37, 47).
One common characteristic among all SIVs is that none are associated with immunodeficiency or any other disease in their natural hosts (9, 13, 22, 28, 30, 35, 38). This finding is in marked contrast to AIDS, which occurs in humans and macaques infected with primate lentiviruses (2, 7, 8, 27, 35). This lack of disease in the natural SIV hosts may be an example of long-term evolution toward avirulence (16), which supports the hypothesis that SIV has infected African simians for a relatively long time.
Human AIDS is caused by two distinct primate lentiviruses, human immunodeficiency virus (HIV), types 1 and 2 (2, 7). Interestingly, the phylogeny of HIV is markedly different from SIV, because genetic analyses have shown that the human viruses do not represent separate sixth and seventh lineages of primate lentiviruses, but instead, are members of two of the five existing SIV lineages (37, 46). HIV-1 is in the HIV-1/SIVcpz group (19, 51) and HIV-2 belongs to the HIV-2/SIVsm family (18, 23). These phylogenetic data on the HIV-1 and HIV-2 lineages have long suggested separate simian origins for HIV-1 and HIV-2 (37, 46).
Molecular studies of naturally occurring SIVsm and HIV-2 strains from rural West Africa have provided convincing evidence for a simian origin of HIV-2. A close genetic relationship has been established between the HIV-2 D and E sub-types and SIVsm strains found in household pet sooty mangabeys in West Africa (4, 14, 15). Moreover, all six known subtypes of HIV-2, including a new subtype F (3), are found only within the natural range of SIV-infected sooty mangabeys in West Africa. No other area of Africa or of the world has all six known HIV-2 subtypes. Together, these data provide strong support for independent transmissions of SIVsm from naturally infected sooty mangabeys to humans.
In contrast, there is much less information to support a simian origin for HIV-1. Although SIVcpz is the closest relative to HIV-1, there are only a few isolates, thus raising questions as to the likely primate reservoir. Only three SIVcpz strains have thus far been identified (20, 41, 42, 51). The first one was isolated from a single, household pet chimpanzee in Gabon and was not part of a primate research colony (42). An additional SIVcpz strain was found in a captive chimpanzee which was wild caught in Zaire and thus likely infected in Africa (41, 51). Finally, PCR data suggested the existence of a third SIVcpz strain, again from a wild caught chimpanzee from Gabon (20). Thus, although based on limited data, the hypothesis that HIV-1 is derived from members of a larger SIVcpz lineage remains plausible. However, additional SIVs within the HIV-1/SIVcpz lineage must be found to better understand the origin of the HIV-1 family.
The present invention is based on the genetic characterization of a new SIV isolate from a red-capped mangabey (RCM), Cercocebus torquatus torquatus. This RCM was a household pet in Lambarene, Gabon, and was not part of a primate colony, a zoo, or a research facility. Analysis of the full-length sequence of the SIVrcm indicates that this virus is related to SIV from sooty mangabeys, albeit very distantly. Its genome organization contains a vpx gene which is unique to members of the SIVsm/HIV-2 lineage. There is also phylogenetic evidence that SIVrcm is a recombinant.
The SIVrcm sequence(s) described herein will permit the development of new serological screening assays for testing of SIVrcm infection of humans. Although such infections have not yet been documented, it should be noted that viruses from a second mangabey species (SIVs from sooty mangabeys) have crossed the species barrier and have yielded a new human AIDS virus (HIV-2). It is thus conceivable that SIVrcm is similarly infecting humans in Gabon and Cameroon. To test this possibility, strain specific reagents (antigens, polypeptides, etc.) are required to test for SIVrcm specific antibodies in people as a sign of viral infection. Such strain specific antigens can now be designed on the basis of the SIVrcm sequence(s) described herein.
If evidence is found that humans in Africa are infected with SIVrcm (regardless whether this infection is pathogenic or not), then new screening assays for the world""s blood supply will have to be developed that specifically detect anti-SIVrcm antibodies or SIVrcm nucleic acids. SIVrcm sequences are necessary to design such strain-specific tests.
Additionally, the new sequences will permit the development of assays for screening of primates, such as those in the wild, in zoos, and in research facilities, for SIVrcm.
The present invention pertains to the isolation and characterization of the genomic sequence of SIVrcm, a new simian immunodeficiency virus identified from a Gabonese red-capped mangabey (RCM), and nucleic acids derived therefrom.
In particular, the present invention relates to nucleic acids comprising the complete genomic sequence of SIVrcm, as well as nucleic acids comprising the complementary (or antisense) sequence of the genomic sequence of SIVrcm, and nucleic acids derived therefrom.
The invention also relates to vectors comprising the nucleic acid genomic sequence of SIVrcm, as well as nucleic acids comprising the complementary (or antisense) sequence of the genomic sequence of SIVrcm, and nucleic acids derived therefrom.
The invention also relates to cultured host cells comprising the nucleic acid genomic sequence of SIVrcm, as well as nucleic acids comprising the complementary (or antisense) sequence of the genomic sequence of SIVrcm, and nucleic acids derived therefrom.
The invention also relates to host cells containing vectors comprising the genomic sequence of SIVrcm, as well as nucleic acids comprising the complementary (or antisense) sequence of the genomic sequence of SIVrcm, and nucleic acids derived therefrom.
The invention also relates to synthetic or recombinant polypeptides encoded by or derived from the nucleic acid sequence of the genome of SIVrcm, and fragments thereof.
The invention also relates to methods for producing the polypeptides of the invention in culture using the SIVrcm virus or nucleic acids derived therefrom, including recombinant methods for producing the polypeptides of the invention.
The invention further relates to methods of using the polypeptides of the invention as immunogens to stimulate an immune response in a mammal, such as the production of antibodies, or the generation of cytotoxic or helper T-lymphocytes.
The invention also relates to methods of using the polypeptides of the invention to detect antibodies which immunologically react with the SIVrcm virion and/or its encoded polypeptides, in a mammal or in a biological sample.
The invention also relates to kits for the detection of antibodies specific for SIVrcm in a biological sample where said kit contains at least one polypeptide encoded by or derived from the SIVrcm nucleic acid sequences of the invention.
The invention also relates to antibodies which immunologically react with the SIVrcm virion and/or its encoded polypeptides.
The invention also relates to methods of detecting SIVrcm virion and/or its encoded polypeptides, or fragments thereof, using the antibodies of the invention.
The invention also relates to kits for detecting SIVrcm virion, and/or its encoded polypeptides, wherein the kit comprises at least one antibody of the invention.
The invention also relates to a method for detecting the presence of SIVrcm virus in a mammal or a biological sample, said method comprising analyzing the DNA or RNA of a mammal or a sample for the presence of the RNAs, cDNAs or genomic DNAs which will hybridize to a nucleic acid derived from SIVrcm. Usually, when a completely complementary probe is used, high stringency conditions are desirable in order to prevent false positives. However, conditions of high stringency should only be used if the probes are complementary to target regions which lack heterogeneity. The stringency of hybridization is determined by a number of factors during hybridization and during the washing procedure, including temperature, ionic strength, length of time, and concentration of formamide, if any. The nucleic acid sequences used in probes should be unique to SIVrcm, i.e., the nucleic acid sequences should be absent from individual mammals not infected with SIVrcm.
The invention also provides diagnostic kits for the detection of SIVrcm in a mammal using the nucleic acids of the invention. In one embodiment, the kit comprises nucleic acids having sequences useful as hybridization probes in determining the presence or absence of SIVrcm RNA, cDNA or genomic DNA. In another embodiment, the kit comprises nucleic acids having sequences useful as primers for reverse-transcription polymerase chain reaction (RT-PCR) analysis of RNA for the presence of SIVrcm in a biological sample.
The invention further relates to isolated and substantially purified nucleic acids, polypeptides and/or antibodies of the invention.
The invention further relates to compositions comprising one or more of the nucleic acids, polypeptides and/or antibodies of the invention.